Genetic Differences Between Humans and Great Apes Ajit Varki Professor of Medicine and Cellular

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Genetic Differences Between Humans and Great
Apes Ajit VarkiProfessor of Medicine and
Cellular Molecular Medicine Co-Director,
Glycobiology Research and Training Center
University of California, San DiegoLa Jolla,
CA, USA
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Homo sapiens sapiens, a recent addition to life
on earth
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10
YEARS BEFORE PRESENT
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Nothing in biology makes sense, except in the
light of evolution.
Theodosius Dobzhansky
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TheProbableEvolution of Life Forms on Earth
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Evolutionary Relationships of Primates and Rodents
Great Apes
New World Monkeys
Old World Monkeys
Rodents
Lesser Apes
Humans
Prosimians
0
10
20
Millions of Years Before Present
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40
50
Precise Timing Uncertain
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Evolutionary Relationships amongst Humans and
the Great Apes

MEAN Amino Acid Difference
0
5
Millions of Years Before Present
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Precise Timing Uncertain
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Wright-stained Normal Human Blood Smear
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Two-Dimensional Separation of proteins The
critical first step in Proteomic Analysis
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Proteomic Comparison of Human and Great Ape Blood
Plasma Reveals Conserved Glycosylation and a
Small Numbers of Differences Gagneux et al.
American Journal of Physical Anthropology 115
99-109, 2001
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Human-specific Blood Plasma Protein Differences
from Great Apes
1 Haptoglobin
2 Transthyretin
Gagneux et al. American Journal of Physical
Anthropology 115 99-109, 2001
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SOME FEATURES OF HUMANS THAT SEEM DIFFERENT FROM
THE GREAT APES
Brain size relative to body Relative size of
neocerebellum of brain growth complete at
birth Age of closure of major fontanelles/sutures
Size of cerebral venous sinuses Age of final
pelvic bone fusion Rotation of the neck of the
astralagus bone Bicondylar angle of the femur
Presence of chin Inner ear canal
orientation Foramen magnum relative to basal
skull axis Adductive thumb Absence of Pharyngeal
Air Sacs Descended larynx Age of first rolling
over Maximum protected life span Skeletal muscle
strength Bone cortex thickness Penis size
relative to body length Penile baculum(penis bone)
Earliest age of onset of menarche Menstrual blood
loss (amount per cycle) Concealed
ovulation Period of sexual receptivity ( of
total cycle) Average Breast tissue mass in virgin
adult female Increase in breast mass during
lactation Modal Chromosome Number Neonatal
Cephalhematoma/caput at birth Menopause Presence
of Ear Lobes Presence of canine tooth
diastema Thickness of tooth enamel Age of first
molar eruption Presence of retromolar
gap Frequency of Third Molar Impaction Body hair
Eccrine/Apocrine sweat gland ratio Dermal fat
thickness (relative to total skin) Relative size
of frontal air sinuses Postnatal body water
change
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Are we really a Third Chimpanzee?
Analysis of 20 structural and functional features
of hominoids (C.Wills A.Varki) presented IN
Children of Prometheus By Chris Wills
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A-Z Examples of Human Uniqueness
Exercise Take a dictionary and check entries
under each letter from the top.
Stop when you reach the first one you think is
unique to humans
Abbreviating Bag-making Calculus Darts Ear-piercin
g Face-lifting Gambling Hacking(computers) Illustr
ating Jet-sking Karate Lacrosse Machining
Nailing(wood) Operating (Surgery) Panning for
gold Quilting Racing (organized) Sacrificing
(others) Tagging (systematic marking) Umpiring Vac
ationing Wage-earning Xeroxing Yachting Zeroing
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Examples of Human Uniqueness starting with the
letter S
Exercise Take a dictionary and scan all entries
under the letter S. Record all
the ones that you think are unique to humans.
Sacrificing Sack-making Saddling Sailing Salt-maki
ng Saluting Sand-castle building Sandwich-making S
awing (wood) Saxaphone playing Schedule
making Schooling Science Scoring
(points) Scuba-diving Sculling Sculpting Sealing
(wax) Selling Semen banking Serum
collecting Sewing Shampooing Shaving
Ship-building Shooting Shopping Signatures Silver
(trading etc.) Singing (e.g., opera) Skating Sketc
hing Skiing Skinning Skipping Sky-diving Slang
words Slavery Sledding Sleighing Slimming Smelteri
ng Snowball fighting Snuff-taking Soaping Sobbing
Soccer Soliciting
Sowing (seeds) Soup making Spaying Spear-throwing
Spelunking Spice collection Spending
_____________ _____________________ ____________
_________ _____________________ ________________
_____ Steel production Stitching Story-telling Su
n-tanning Surfing
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DNA RNA PROTEIN
CELL ORGANISM
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ORGANISM
PHYSICAL ENVIRONMENT
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BIOLOGICAL ENVIRONMENT
Microbes
ORGANISM
PHYSICAL ENVIRONMENT
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BIOLOGICAL ENVIRONMENT
CULTURAL ENVIRONMENT
ORGANISM
PHYSICAL ENVIRONMENT
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BIOLOGICAL ENVIRONMENT
CULTURAL ENVIRONMENT
ORGANISM
HUMANS
HUMANS
PHYSICAL ENVIRONMENT
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DNA
RNA
PROTEINS
ORGANISM
DNA
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Wright-stained Normal Human Blood Smear
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Scanning Electron Micrograph of Human Red Blood
Cells
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Scale Model of 1/100,000 of Human Red Blood Cell
Surface
Sialic Acid
Neutral Sugars
Protein
Modified from Viitala Järnefelt
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Biological Roles of Sialic Acids
Structural/Physical Roles
SELF
SIALIC ACID CARRYING SUGAR CHAIN
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(1984) UCSD Medical Center Sarah Anna
Varki
HEMATOLOGY CONSULT Case A 22-year old woman
with weakness and bleeding. Diagnosis Aplastic
Anemia (bone marrow failure) Treatment Trial of
Equine Anti-Thymocyte Globulin (Horse
Serum) Complication Serum Sickness Reaction to
Horse Serum Immune Reaction partly
against Sialic Acids in Horse Serum!
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Two major kinds of Sialic Acids in Mammals
Neu5Ac and Neu5Gc
Human Cells are Unusual Excess of Neu5Ac and
Loss of Neu5Gc
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Neu5Ac Neu5GcHumans
-Great Apes
Sialic acids on Red Cells and Plasma Proteins
from Humans and Great Apes
Muchmore, E.A., Diaz, S. Varki, A.
Amer.J.Physical Anthropology 107187-198,1998 (Gre
at Ape samples from Yerkes Primate Center,
Atlanta, GA)

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

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Evolutionary Relationships amongst Humans and
the Great Apes

MEAN Amino Acid Difference
0
5
Millions of Years Before Present
10
Precise Timing Uncertain
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Neu5Ac Neu5GcHumans
-Great Apes

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

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MANY BIOLOGISTS ASSUME THAT EVOLUTION USUALLY
RESULTS IN OPTIMAL DESIGN
CREATIONISTS
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Human-Specific Loss of Neu5Gc (CMAH mutation)

• Random mutation that drifted to fixation due to
  small effective population size?
• Selection due to Neu5Gc-recognizing pathogen(s)?
• Signature of other past selective sweep
  affecting hominid ancestors?
• Regardless of the cause, what were the
  consequences for human evolution?

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Neu5Ac Neu5GcHumans
-Great Apes

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

CMAH Mutation found in Homozygous State in all
Human Populations studied
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Modern Humans - a very recent success story
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Modern Humans - a very recent success story
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Modified from Bernard Wood, Nature, 418133-5,
2002
Java Man
Lucy
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Neu5Ac Neu5GcHumans
-Great Apes

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

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Biological Roles of Sialic Acids
Structural/Physical Roles
SELF
SIALYLATED OLIGOSACCHARIDE
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Neu5Ac Neu5GcHumans
-Great Apes

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

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Biological Roles of Sialic Acids
Structural/Physical Roles
SELF
SIALYLATED OLIGOSACCHARIDE
41
Neu5Ac Neu5GcHumans
-Great Apes

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

42
Neu5Ac Neu5GcHumans
traceGreat Apes

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

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Uptake and Excretion of Neu5Gc in Normal Humans
Intensity
Detection by DMB-HPLC and Mass Spectrometry
Elaine Muchmore Sandra Diaz Pascal
Gagneux
Tangvoranuntakul et al. Proc.Nat'l.Acad.Sci.U.S.A.
10012045-12050, 2003
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Distribution of Neu5Gc in Common Foods

• Fruits, vegetables and grains - none?
• (no sialic acids)
• Chicken and Turkey - traces
• Fish - variable, but very low
• Bovine milk and milk products - low
• Lamb, Pork and Beef - high

Sandra Diaz Pascal Gagneux
Tangvoranuntakul et al. Proc.Nat'l.Acad.Sci.U.S.A.
10012045-12050, 2003
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Detection of Anti-Neu5Gc antibodies in Normal
Human Sera
Pam Tang Pascal Gagneux
A492
Frequency much higher than previously
reportedLikely due to improved assay with lower
background and better negative controlsHigher
values are in range for anti-alpha-Gal antibodies
Tangvoranuntakul et al. Proc.Nat'l.Acad.Sci.U.S.A.
10012045-12050, 2003
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Neu5Ac Neu5GcHumans
-Great Apes

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

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Neu5Ac Neu5GcHumans
tracesGreat Apes

• The Human Loss of
  Neu5Gc Expression
• HOW did it happen?
• WHY did it happen?
• WHEN did it happen?
• WHAT are the consequences for risk of infections
  in humans?
• WHAT are the consequences for human sialic acid
  receptors?
• HOW does Neu5Gc re-expression in tumors and
  fetuses occur?
• WHERE does the small amount of Neu5Gc in humans
  come from?
• WHAT are the consequences of human ingestion of
  Neu5Gc in food?
• WHAT are the consequences for biotechnology
  products?
• WHAT are the consequences for attempts at
  xenotransplantation?
• WHAT are the consequences for the human brain?

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Even Mammals With High Levels of Neu5Gc in
Non-neural Tissues, it is Difficult to Detect
Neu5Gc in the Brain
Pascal Gagneux
CMAH gene expression is down-regulated in
mammalian brains
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Multiple Human-Specific Changes in Sialic Acid
Biology - What do they mean?

• Random mutations that have drifted to fixation
  due to small effective population size?
  Unlikely, too many changes.
• Selection due to Neu5Gc-recognizing pathogen(s)?
• Signature of a past selective sweep affecting
  hominid ancestors? Likely - cause or
  consequence?
• What are consequences for humans today?
• Innate immune system?
• Susceptibility/resistance to pathogens?
• Brain development?
• Dietary ingestion of Neu5Gc?
• Biotechnology and Xenotransplantation?

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Multiple Differences in Sialic Acid Biology
Between Humans Great Apes
Genomic mutation in CMP-Neu5Ac Hydroxylase
(CMAH)
Definite
Difference
Probable
Possible
Homozygosity of CMAH mutation
Point mutation Eliminating critical arginine
residue in Siglec-L1
Altered regulation of ST6Gal-I gene expression
(promoter mutation?)
Human expression of a2-6-linked Sias on bronchial
epithelium and certain other cell types and loss
of expression on goblet cells
Susceptibility to Human Influenza Strains
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• McConkey E. H., and M. Goodman. 1997. A Human
  Genome Evolution Project is needed. Trends Genet.
  13350-351.
• Vigilant L., and S. Paabo. 1999. A Chimpanzee
  Millennium Biol Chem. 3801353-1354.
• McConkey E. H., R. Fouts, M. Goodman, D. Nelson,
  D. Penny, M. Ruvolo, J. Sikela, C. B. Stewart, A.
  Varki, and S. Wise. 2000. Proposal for a Human
  Genome Evolution Project. Mol Phylogenet Evol.
  151-4.
• McConkey E. H., and A. Varki. 2000. A Primate
  Genome Project deserves high priority. Science.
  2891295-1296. Co-signatories John Allman, Kurt
  Benirschke, Terrence W. Deacon, Frans de Waal,
  Achilles Dugaiczyk, Pascal Gagneux, Morris
  Goodman, Lawrence I. Grossman, Deborah Gumucio,
  Thomas Insel, Kenneth K. Kidd, Mary-Claire King,
  Kenneth Krauter, Raju Kucherlapati, Arno G.
  Motulsky, David Nelson, Peter Oefner, George
  Palade, Maryellen Ruvolo, Oliver A. Ryder, James
  Sikela, Caro-Beth Stewart, Anne Stone , David
  Woodruff.
• Varki A. 2000. A chimpanzee genome project is a
  biomedical imperative. Genome Res. 101065-1070.

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Apparent Differences between Humans and Great
Apes in the Incidence or Severity of Medically
Important Conditions(Excluding those explained
by obvious anatomical differences)
MEDICAL CONDITION HUMANS GREAT APES HIV
progression to AIDS Common Very rare P.
falciparum Malaria Susceptible Resistant Menopause
Universal Rare Simian Foamy virus
Infection Rare Common Alzheimers Disease
pathology Complete Incomplete Influenza A
symptomatology Moderate to Severe Mild Myocardial
Infarction (Heart Attack) Common Uncommon Hepatiti
s B/C late complications Moderate to
Severe Mild Epithelial Cancers Common Rare? E.coli
K99 Gastroenteritis Resistant Sensitive? Menstrua
l Blood Loss Variable Lower amount? Early Fetal
Wastage High Low? Bronchial Asthma Common Rare? Au
toimmune Diseases Relatively Common Rare? Acne
Vulgaris Common Rare? Major Psychoses Common Rare?
Olson, M. Varki A. Nature Reviews Genetics.,
4 20-28, 2003 Varki, A. Genome Research
101065-1070, 2000.
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Reasons for Sequencing the Chimpanzee Genome

• Explaining Features of the Human Condition
• Explaining Biomedical Differences
• between Humans and Chimpanzees
• Improving the Care Conservation of Chimpanzees
  in Captivity

Need other Primate Genomes to fully interpret
differences
Need to check differences in multiple
individuals
Need attention to Ethical, Legal and Social Issues
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• Primate Genomics Workshop, Seattle, WA, January,
  2001 (Organizers William R. Morton, Michael G.
  Katze Roger Bumgarner)
• GEMINI Genes and Minds Initiative -- Workshop on
  Ape Genomics, March 14-15, 2001, Tokyo
  (organizers Yoshiyuki Sakaki, Naruya Saitou,
  Nobuyuki Nukina)
• Olson, M. V., Eichler, E. E., Varki, A., Myers,
  R.M., Erwin, J. M., and McConkey, E. H. A White
  Paper Advocating Complete Sequencing of the
  Genome of the Common Chimpanzee, Pan Troglodytes 
  (White paper submitted to NHGRI, February 2001).
• Reich, D.E., Lander, E. S., Waterston, R., Pääbo,
  S., Ruvolo, M., and Varki, A. Sequencing the
  Chimpanzee Genome (White paper submitted to
  NHGRI, February 2001).
• Olson, M. and Varki A. Sequencing the Chimpanzee
  Genome Insights into Human Evolution and
  Disease Nature Reviews Genetics., 4 20-28, 2003.

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NHGRI News Release Dec. 10, 2003 Chimp Genome
Assembled by Sequencing Centers Draft Sequence
Aligned With Human GenomeThe sequence of the
chimpanzee, Pan troglodytes , was assembled by
NHGRI-funded teams led by Eric Lander, Ph.D., at
The Eli Edythe L. Broad Institute of the
Massachusetts Institute of Technology and Harvard
University, Cambridge, Mass. and Richard K.
Wilson, Ph.D., at the Genome Sequencing Center,
Washington University School of Medicine,
Saint Louis.
http//www.nhgri.nih.gov/11509418
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Great Ape Phenome Project? Science 282, 239-240
(1998)Varki, A., Wills, C., Perlmutter, D.,
Woodruff, D., Gage, F., Moore, J., Semendeferi,
K., Benirschke, K., Katzman, R., Doolittle, R.
Bullock, T.

• Much to be learned by comparing human genomic
  sequences with..those of our closest
  evolutionary cousins, the great apes.
• Part of the value of the Human Genome Project
  lies in interpreting genomic data in the context
  of the large body of existing information about
  humans.
• Corresponding information about the great apes is
  limited.
• Funding of a Great Ape Genome Project should be
  complemented by a "Great Ape Phenome Project," .
  comparative studies of humans and apes at all
  levels, from expression patterns of mRNA, to
  biochemistry and cell biology, all the way to
  neural systems and cognitive functions.
• Significance of most genomic sequence differences
  found between humans and apes will not be obvious
  unless such a detailed comparative phenotypic
  database is also available.
• Could be obtained without harm to primates, using
  ethical principles similar to those guiding human
  experimentation.
• Project would also heighten awareness of the
  urgent need to protect and conserve these
  endangered hominoids who are so closely related
  to us.

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GenomeA haploid set of chromosomes the
sum-total of the genes in such a set(Oxford
English Dictionary, 2003)orthe complete genetic
material of an organism
Phenome (no entry in any Dictionary)
(but 27,200 entries now in Google)Suggested
Definition Complete information about an
organisms phenotype and the relevant
environmental influences
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Interactions of Genotype and Phenotype
Genotype
Phenotype
ENVIRONMENT
Compare
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Acknowledgments

• Members of the lab
• Collaborators
• UCSD
• NIH, Mathers Foundation
• Colleagues in
• Glycobiology Research and Training Center
• Project for Explaining the Origin of Humans

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